Paratuberculosis (PTB) is a contagious and chronic enteric disease of ruminants and many non-ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), and is characterised by diarrhoea and progressive emaciation with consequent serious economic losses due to death, early culling, and reduced productivity. In addition, indirect economic losses may arise from trade restrictions. Besides being a production limiting disease, PTB is a potential zoonosis; MAP has been isolated from Crohn’s disease patients and was associated with other human diseases, such as rheumatoid arthritis, Hashimoto’s thyroiditis, Type 1 diabetes, and multiple sclerosis. Paratuberculosis in sheep and goats may be globally distributed though information on the prevalence and economic impact in many developing countries seem to be scanty. Goats are more susceptible to infection than sheep and both species are likely to develop the clinical disease. Ingestion of feed and water contaminated with faeces of MAP-positive animals is the common route of infection, which then spreads horizontally and vertically. In African countries, PTB has been described as a “neglected disease”, and in small ruminants, which support the livelihood of people in rural areas and poor communities, the disease was rarely reported. Prevention and control of small ruminants’ PTB is difficult because diagnostic assays demonstrate poor sensitivity early in the disease process, in addition to the difficulties in identifying subclinically infected animals. Further studies are needed to provide more insight on molecular epidemiology, transmission, and impact on other animals or humans, socio-economic aspects, prevention and control of small ruminant PTB.

Three experiments were conducted to study the effects of dietary potassium intake on magnesium metabolism. In experiment 1, 24 wether lambs were used in two metabolism trials to determine the minimum level of potassium that depresses magnesium absorption. Two magnesium levels (.1 and .2%) were fed with four levels of potassium (.6, 1.2, 2.4 and 4.8%) in a 2 x 4 factorial arrangement of treatments. Each trial consisted of a 10-day preliminary period followed by a 10-day collection period. Greater amounts (P<.05) of magnesium were absorbed and retained when animals were fed the high level of magnesium (.2%). Increasing the level of potassium in the diet increased (P<.05) fecal magnesium excretion. Magnesium absorption decreased linearly with increasing levels of potassium. The greatest depression in magnesium absorption occurred when the potassium level was increased from 1.2 to 2.4%. A further large decrease in absorption occurred when the potassium level was increased from 2.4 to 4.8%. Serum magnesium was depressed when higher levels of potassium were fed. Potassium absorption was not affected by level of dietary magnesium, but increased (P<.05) with increasing levels of dietary potassium. In experiment 2, two metabolism trials were conducted with 18 wether lambs, equipped with abomasal and ileal cannulae, in a 2 x 3 factorial arrangement. Two levels of magnesium (.1 and .2%) and three levels of potassium (.6, 2.4, and 4.8%) were used. Chromic oxide was used as an indicator to determine digesta flow. Each trial consisted of a 10-day preliminary period, a 7-day collection of feed, feces and urine, and a 6-day sampling of feed, abomasal and ileal fluid and feces. Magnesium was absorbed mainly prior to reaching the small intestine, followed by a low net absorption in the large intestine. Increasinq potassium level resulted in a linear decrease in magnesium absorption. Preintestinal magnesium absorption decreased (P<.05) with each increase in dietary potassium. Large amounts of magnesium flowed into the small and large intestines and was excreted in the feces when higher levels of potassium were fed. Lambs fed the high level of magnesium (.2%) absorbed larger amounts of magnesium from the stomach. Magnesium absorbed, expressed as a percent of intake, was not affected by level of magnesium. Experiment 3 consisted of three metabolism trials with six Angus x Simmental steer calves, per trial, equipped with abomasal and ileal cannulae. Steers were fed .1% magnesium and three levels of potassium, .6, 2.4 and 4.8%. Procedures were similar to those used in Experiment 2. Magnesium absorption decreased linearly (P<.05) when high levels of potassium were fed. The primary site of magnesium absorption was the preintestinal region, followed by a net secretion into the small and large intestines. Preintestinal magnesium absorption was decreased approximately 50% when steers were fed 4.8% potassium. Small amounts of magnesium tended to be secreted into the small intestine when the high level of potassium was fed. As observed in experiment 1, serum magnesium levels were depressed when increasing amounts of potassium were fed. Potassium absorption increased with increasing levels of dietary potassium. The effect of high dietary potassium on magnesium absorption was similar to those reported in experiments 1 and 2 with sheep. / Ph. D.

Five crossbred heifers were slaughtered at different times and rumen and omasum tissues were removed: The epithelium was separated from the muscle layer and mounted in parabiotic chambers. The tissues were incubated for 2 h in buffer at 39 C and aerated continuously in 95% O₂ 5% CO₂ . The buffers were similar to those which have been used previously in mineral transport studies, but were modified by varying the levels of Mg and K while keeping the osmolarity constant. Potassium was included in the buffers on the mucosal side in appropriate ratios to Mg to correspond to the K: Mg in diets fed to ruminants which would contain .1% Mg and .6, 2.4 and 4.8% K, (low, medium and high, respectively). A fourth buffer which contained physiological concentrations of Kand Mg, was placed on the serosal side of the parabiotic chamber. Flow of Mg was calculated by: F = C₁V₁ - C₀V₀ / AΔt where C₁ = final concentration, C₀ = original concentration, V₁ = final volume, V₀ = original volume, Δt = incubation time, A = area of the tissue exposed to the buffer, and F = flow of Mg (mg/cm²/h). Blanks were included which contained physiological levels of Mg on both side of the chamber to adjust for tissue effects. Magnesium transport tended to be 10 times greater through the rumen than the omasum. This indicates that the rumen is the primary site of Mg absorption in cattle. Potassium tended to depress Mg transport across both tissues. This technique has only limited application in mineral research. / M.S.

Le groupe ‘M. mycoides’ constitue une branche phylogénétique homogène des mycoplasmes regroupant 6 taxons pathogènes des ruminants, responsables pour la plupart de maladies inscrites sur la liste de l’OIE. L’identification taxinomique sur laquelle repose le diagnostic reste délicate à cause de réactions antigéniques et génétiques croisées et d’un manque d’universalité intra-taxon des PCR, notamment pour les taxons Mcc, MmmLC et Mbg7. Une approche par hybridation soustractive sélective a été développée pour 1) appréhender les différences moléculaires entre ces 3 taxons ; 2) analyser globalement la diversité au sein du groupe ‘M. mycoides’ et 3) rechercher de nouveaux marqueurs d’intérêt diagnostique. Nos résultats montrent un important partage de séquences entre ces taxons, MmmLC et Mcc étant très polymorphes par rapport à Mbg7, plus homogène et qui représente une sorte de chimère entre les taxons Mcc et MmmSC. Nos données nous ont permis de développer un test PCR spécifique pour Mcc mais la diversité génétique du groupe ‘M. mycoides’ dépasse les frontières entre taxons rendant difficile et peu pertinente l’identification taxinomique. Un typage des souches en fonction de la virulence indépendamment de l’espèce serait l’approche diagnostique alternative. La faisabilité d’une telle approche a été explorée dans le cas du taxon MmmLC mais aucun critère susceptible de différencier les souches issues de foyers de celles issues de portage dans des troupeaux sans antécédent clinique n’a pu être mis en évidence. Ce continuum génétique entre souches, probablement lié à des transferts génétiques horizontaux, imposera à l’avenir une surveillance globalisée des mycoplasmoses / The ‘M. mycoides’ cluster, a homogenous phylogenetic branch of the Mollicutes, includes 6 taxa which are responsible for diseases in ruminants, most of which are listed by the OIE. Their taxonomic identification, on which current diagnosis is based, is impaired by antigenic and genetic cross-reactivity and by the lack of a universal, intra-taxon PCR assay, especially for the Mcc, MmmLC and Mbg7 taxa. A suppression subtractive hybridization approach was developed to: 1) define molecular differences between these 3 taxa; 2) analyze the overall genetic diversity within the ‘M. mycoides’ cluster and 3) search for new markers useful for diagnosis. Results obtained here showed that several sequences are shared across taxa, with Mcc and MmmLC being very polymorphic compared to Mbg7 which is more homogeneous, representing a sort of chimera between Mcc and MmmLC. From these analyses, a specific PCR assay was designed for Mcc identification but, because of the genetic diversity existing within the ‘M. mycoides’, the taxonomic identification of new strain appears less and less relevant. Instead, regardless of their species, strain typing on the basis of their virulence would offer an alternative approach for diagnosis. We assessed this type of approach for the MmmLC taxon but so far, our attempts to uncover markers that would distinguish pathogenic strains from carrier strains, isolated from herds with no clinical history, have failed. The genetic continuum observed between strains is remnant of horizontal gene transfers and imposes the development of a more global approach for mycoplasmosis surveillance

Le virus Schmallenberg (SBV) appartient au genre Orthobunyavirus, au sein de la famille des Bunyaviridae. Ce nouveau virus, découvert en 2011 au nord-ouest de l’Europe, affecte les ruminants domestiques. Il est responsable de signes cliniques discrets chez les adultes et de malformations congénitales chez les nouveau-nés. Ces travaux de thèse s’inscrivent dans les projets d’étude de la pathogenèse de l’infection à SBV et de l’épidémiologie de la maladie, dans le cadre d’un programme de recherche européen sur le virus. Ce manuscrit inclut de nouvelles données, telles les cinétiques de la virémie et de la séroconversion chez les ovins et caprins, après infection expérimentale par SBV. La possibilité d’infection par SBV par voie vaginale est démontrée expérimentalement chez la chèvre. Après infection expérimentale de chèvres gestantes entre 28 et 42 jours de gestation, une mortalité fœtale ou des lésions du système nerveux central des fœtus peuvent survenir. Enfin, la sensibilité de plusieurs espèces de ruminants sauvages et exotiques de parcs zoologiques vis-à-vis de SBV est démontrée pour la première fois. / Schmallenberg virus (SBV) belongs to the genus Orthobunyavirus in the family Bunyaviridae. This new virus was discovered in 2011 in Northwestern Europe in domestic ruminants. Infection by SBV is associated with mild clinical signs in adult and congenital malformations in the progeny. In the scope of the European research program on SBV in the pathogenesis and epidemiology areas, the works included in this thesis provide new data about SBV infection in livestock and wild and exotic ruminants. The kinetics of viremia and seroconversion after experimental SBV infection are described in sheep and goats. This manuscript includes evidence of SBV infection via vaginal route in goats. Experimental SBV infection in pregnant goats between 28 and 42 days of gestation can lead to death or central nervous system lesions in fetuses. Evidence of susceptibility to SBV in several species of wild and exotic ruminants kept in zoos is described for the first time.

Mycoplasma agalactiae est responsable de l'agalactie contagieuse, maladie des petits ruminants difficilement contrôlée et figurant sur la liste de l’OIE. Afin d’évaluer la diversité génétique de ce pathogène, 101 isolats ont été comparés par trois techniques (VNTR, RFLP, répertoire vpma). Les résultats révèlent une grande homogénéité génétique dont la souche type PG2 est représentative. Quelques isolats font exception telle la souche 5632 que nous avons séquencée et analysée ici. La comparaison des génomes et des protéomes entre 5632 et PG2 indiquent que la plasticité de ces génomes est liée à d’importants échanges d'ADN et à la présence de nombreux éléments génétiques mobiles (10% du génome). Ces analyses révèlent également une forte dynamique au sein de répertoires de gènes codant des protéines de surfaces. Pour les mycoplasmes, bactéries minimales dépourvues de paroi, ces évènements ont certainement joués un rôle dans leur survie et leur adaptation à des hôtes complexes. / Mycoplasma agalactiae is responsible of contagious agalactia, a disease of small ruminants that is still difficult to control and is listed by the OIE. In order to evaluate the genetic diversity of this pathogen, 101 isolates were compared using three techniques (VNTR, RFLP, vpma repertoire). Results revealed a high genetic homogeneity with the PG2 type strain as representative. Some isolates however diverged such as the 5632 which was sequenced and analysed here. Whole comparative genomic and proteomic analyses of the 5632 and PG2 strains indicate that their genomic plasticity resides in important genes flux and in the presence of several mobile genetic elements (10% of the genome). These analyses also revealed that specific loci encoding repertoire of surface proteins are highly dynamic. For these minimal bacteria that lack a cell-wall, these events have most likely played a major role in their survival and adaptation to complex hosts.

The current research was done to evaluate the nutritive values and the ruminal degradation of dry matter (DM) and crude protein (CP) from three non-conventional oil cakes, viz: amarula (Sclerocarya birrea) (AOC), macadamia (Integrifolia) (MOC) and baobab (Adansonia digitate L.) (BOC). The oil cakes were collected from biodiesel producers in Limpopo Province, transported to the ARC-Animal Production campus, where proximate and ruminal nutrient degradation analysis were conducted. Triplicates samples from each oil cake were analyzed for the nutritive values, mineral and amino acids contents. Three rumen cannulated mid-lactating (days in milk; DIM: 180±5) Holstein cows weighing 667±43 kg body weight were allocated to determine the in situ ruminal dry matter (DM) and crude protein (CP) degradation. The cows were offered a totally mixed ration (TMR) (60 concentrate: 40 forage ratio) that was compounded according to their daily nutrient requirements, and were milking was done twice per day at 12 hrs intervals. The three oil cake samples were ground using a 2-mm screen after which sub-samples (6.5 g) were put in 10 x 20 cm; 50 μm pore size polyester bags to achieve 15 mg/cm² (ratio of the sample size to surface area). The bags were then fistulated in each cow’s rumen in triplicate for a period of 2, 4, 8, 16, 24, or 48 hrs. After being incubated, the bags were removed from the rumen and washed with cold (4°C) water in 20-L buckets. Following immersing in cold water, the bags were machine washed until clean water was obtained. The bags were then dried at 60 °C in an oven for 48 hrs. The dried bags were individually weighed, and the content of each bag were removed and stored into glass vial until analysis. The remaining two duplicate sets of each sample were rinsed using cold water in order to determine solubility at 0 hrs. The AOC had higher (P<0.05) ether extract (EE) and CP content than both BOC and MOC. Macadamia oilcake (MOC) and BOC had higher (P<0.05) fractions of fibre (NDF, ADF and ADL) compared to the AOC. The AOC had greater (P<0.05) content of essential amino acids than in the BOC and MOC. Additionally, AOC had a high (P<0.05) phosphorus, but low calcium and potassium concentration. While AOC had high effective degradability of DM, it also had high water soluble as well as DM and CP rapidly degradable fractions. Effective degradation of CP was higher in AOC and BOC than in MOC. However, BOC had a high insoluble but degradable fraction of CP. Further work to determine the toxicology of these non-conventional oil cakes and animal feeding experiments is needed / Agriculture and  Animal Health / MSc. Agriculture

[Truncated abstract] Antimicrobial growth promoters are added to feed to prevent lactic acidosis in ruminant animals by selectively inhibiting rumen bacteria that produce lactic acid. However, recently imposed or impending bans on the use of antimicrobial growth promoters in animal production have lead to a critical need to find practical alternatives that are safe for the animal and consumer and that obtain similar production benefits. I investigated bioactive plants of Australia for their potential to prevent lactic acidosis in ruminants. The unifying hypothesis tested was that plants would be identified that selectively inhibit lactic acid-producing bacteria and consequently protect against lactic acidosis. This hypothesis was tested in a three phase process: phase 1, plant selection and collection; phase 2, a three stage protocol for screening plants and essential oils; phase 3, in vivo experiments and chemical fractionation of the most promising plant. I developed an in vitro bioassay that simulated acidosis by adding glucose to rumen fluid in Bellco tubes and incubating for 5 h (Chapter 4). The pH and gas production were used as indicators of acidosis and fermentation activity. I used this bioassay to screen ninety-five plants (dried and ground material from 79 species) and ten essential oils and included a negative control (oaten chaff) and a positive control (virginiamycin). One plant, Eremophila glabra, produced a similar pH (5.63) to the positive control (5.43) although it inhibited gas production to a moderate extent (P < 0.05). ... Seven serrulatane diterpenes were identified to be the major secondary metabolites in E. glabra. The metabolites were screened using a broth dilution and microtitre spectrophotometry method and were selective against S. bovis at between 320 and 1077 [mu]g/ mL. The serrulatanes from E. glabra were probably responsible for the activity against acidosis that I observed in vitro, because they selectively inhibited lactateproducing bacteria. It is also possible that a synergy between serrulatanes and possibly other metabolites are responsible for the activity observed in vitro. The results from my experiments support the role that bioactive plants may have to replace the antibiotics that are added to livestock feed. Australian plants were identified containing compounds that were active against the bacterial processes responsible for ruminant acidosis. To my knowledge this is the first work undertaken to identify bioactive plants of Australia for their potential to prevent acidosis. I developed in vitro screening bioassays that targeted key indicators of acidosis. These bioassays enabled me to identify 5 plants from the 104 screened that could potentially control acidosis. One of these plants in particular, E. glabra, showed a level of activity in vitro that was comparable to antibiotic protection against acidosis. The exciting in vitro results were not demonstrated in vivo but only one dose level of E. glabra was used, which was based on the in vitro work. In contrast to the in vitro system the rumen is a continuous flow system with greater complexity and it is possible that the concentration of E. glabra that I used in vivo was not optimum. This places importance on future dose response experiments to confirm the efficacy of E. glabra in vivo.

Wenn auf dem Foto oben der Westwind Zephyr und in seinen Armen die Morgenbrise Aura nicht Venus an die Gestaden Zyperns treibt, sondern stattdessen den Geburtstagskuchen ausbläst , dann ist sein Atem das, was in der Strömungsmechanik als „laminare Strömung“ bezeichnet wird. Eine Strömung, deren Stromlinien parallel zueinander verlaufen und deren Einzelelemente, hier die Luftmoleküle, einen gleichgerichteten Weg verfolgen. „Turbulent“ ist hingegen der von den Kerzen aufsteigende Rauch über dem Kuchen, der „Richtung Osten“ hinweggeblasen wird. Diese Turbulenz von Flüssigkeiten und Gasen ist allgegenwärtig in unserer Welt, ob für unser Auge direkt sichtbar oder unsichtbar: die Luft, die tief in unsere Lunge eingesogen wird bis hin zu den Lungenbläschen, die Spuren der Milch beim Umrühren in einer Kaffeetasse, der Rauch, der von einem Schornstein aufsteigt, das Wasser rund um die großen und kleinen Kiesel in einem Bach, der Wind, der den Kirchturm und die Hausecke umwirbelt, das heiße Plasma, das in Feuerfackeln von der Sonnenoberfläche ins Weltall hinauslodert, oder die großen Wolken kosmischen Staubs, die sich in Strudeln und Wirbeln zu Galaxien oder Sternen verdichten. „Turbulent“ ist also eine Strömung, deren Stromlinien sich zu überkreuzen scheinen und deren Einzelelemente keinen gleichgerichteten Weg verfolgen. Stattdessen existieren vielfältigste Formen und Muster von miteinander verschränkten Wirbeln auf allen Größenskalen. Aufgrund dieser Komplexität in Formen und Skalen gehört die Beschreibung und Vorhersage von Turbulenz schon seit Jahrhunderten zu den großen Rätseln in Physik und Mathematik. Da turbulente Strömungen gleichwohl derart zentral sind für viele Bereiche menschlichen Lebens und Handelns, werden Grundlagen- und Anwendungsforschung mit Nachdruck vorangetrieben. Die vorliegende Arbeit umfaßt gleich drei Anwendungsfälle von Turbulenzforschung, und es darf als bezeichnend für die Allgegenwart der Turbulenz angesehen werden, daß sich diese drei Anwendungen in solch unterschiedlichen Größenskalen abspielen. Die Windabkühlung von Rindern, die bis in den Sub-Millimeter-Maßstab im Bereich von Fell und Hautoberfläche hinein betrachtet werden muß, die Sturmge-fährdung von Wäldern, für die Größen zwischen einem halben Meter an den Bäumen und mehreren Kilometern in der Landschaft relevant sind, und zu guter Letzt das turbulente Geschehen in kos-mischen Gaswolken und Galaxienhaufen, das sich im Größenbereich von vielen Millionen Lichtjahren abspielt. Nicht nur in den Techniken der Modellierung, sondern auch in der physikalischen Wirklich-keit sind diese Phänomene trotz der gewaltigen Größenunterschiede eng verwandt. In diesem Sinne: vom Kosmos zur Kuh.

The rumen microbiome constitutes a unique genetic resource of plant fiber degrading microbial enzymes that could be used for agricultural and industrial purposes. Anaeromyces mucronatus is a poorly characterized anaerobic lignocellulolytic fungus in the rumen. This thesis aimed at better understanding A. mucronatus YE505 and the particle associated rumen microbiota based on transcriptomic and metatranscriptomic approaches. High quality RNA was isolated from the fiber-associated rumen sample based on an improved RNA extraction method. A transcriptomic study was performed to investigate the expression of the fiber degrading system of A. mucronatus YE505, and the functional diversity of the fiber-associated eukaryotes from the rumen of muskoxen (Ovibos moschatus) was explored by a metatranscriptomic study. Much carbohydrate degradation related protein modules were detected. This study established effective approaches to characterizing the functional contents of rumen eukaryotic microbiome as well as rumen fungi, and identified several candidate genes that merit further investigation. / xiv leaves : ill. (some col.) ; 29 cm